File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/41b959c8e4dbb9787d2ccf86d97fb2/.command.log
Size
57.1 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (tih_rna_sample_00451_B23WHTKLT4_1)
Attempt

Content

View in new tab 
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/3dc495e1a9f1e69d9d787dec0d61f4/tih_rna_sample_00451_B23WHTKLT4_1_2.fastp.fastq.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/41b959c8e4dbb9787d2ccf86d97fb2/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/41b959c8e4dbb9787d2ccf86d97fb2/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/3dc495e1a9f1e69d9d787dec0d61f4/tih_rna_sample_00451_B23WHTKLT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/4e0a4f0f41868724dc5f45313032ca/tih_rna_sample_00451_B23WHTKLT4_1.fusionreport.tsv
==> STAGING COMPLETE (6 inputs)

Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00451_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.Bsc2MN2IDn/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.Bsc2MN2IDn/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1 --shrink_introns --max_intron_length 1000 
Done.
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00451_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.Bsc2MN2IDn/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.Bsc2MN2IDn/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.fa /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.fa /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fa
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.gtf /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.gtf /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.gtf
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.fa /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.gtf > /tmp/nxf.Bsc2MN2IDn/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.fa /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.gtf > /tmp/nxf.Bsc2MN2IDn/cytoBand.txt
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.gtf > /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.bed
-parsing GTF file: /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.gtf > /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.bed
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.bed > /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.bed > /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/tih_rna_sample_00451_B23WHTKLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/tih_rna_sample_00451_B23WHTKLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/tih_rna_sample_00451_B23WHTKLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.fa
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.Bsc2MN2IDn/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00451_B23WHTKLT4_1.star --out_dir /tmp/nxf.Bsc2MN2IDn/fi_workdir --reads "/tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.Bsc2MN2IDn/ctat_genome_lib_build_dir/ref_genome.fa.star.idx  --outSAMtype BAM SortedByCoordinate  --twopassMode None  --alignSJDBoverhangMin 10  --genomeSuffixLengthMax 10000 --limitBAMsortRAM 47271261705  --alignInsertionFlush Right   --alignMatesGapMax 100000  --alignIntronMax 100000  --outSAMattributes All  --readFilesIn /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 08 10:11:43 ..... started STAR run
Jun 08 10:11:43 ..... loading genome
Jun 08 10:13:27 ... generating Suffix Array index
Jun 08 10:17:21 ... completed Suffix Array index
Jun 08 10:17:21 ..... processing annotations GTF
Jun 08 10:17:22 ..... inserting junctions into the genome indices
Jun 08 10:18:22 ..... started mapping
Jun 08 11:28:04 ..... finished mapping
Jun 08 11:28:06 ..... started sorting BAM
Jun 08 11:28:06 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00451_B23WHTKLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00451_B23WHTKLT4_1.star.sortedByCoord.out.bam
Execution Time = 76.40 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.Bsc2MN2IDn/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00451_B23WHTKLT4_1.star --out_dir /tmp/nxf.Bsc2MN2IDn/fi_workdir --reads "/tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
11:28:11 : INFO : Done.
Execution Time = 0.07 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/mark_dups_reads.index.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.gtf
-parsing /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.star.cSorted.dupsMarked.bam

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[830000]   -done parsing /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
          'low complexity anchor region' => 21,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 24,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 30,
          'seq-similar region overlap' => 655,
          'num genes matched < 2' => 12,
          'excessive soft clipping' => 4139,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 32,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
          'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 20,
          'num_hits: 7 != num_counted_on_fusion_contigs 5 ' => 90,
          'per_id < 96' => 3235,
          ' ** passed ** ' => 6514,
          'small anchor length' => 58,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 1,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 15
        };
-writing fusion junction support info.
Execution Time = 0.41 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[55000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13

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[61000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1

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[48000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2

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[64000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHA13

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[70000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC1

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[58000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC2

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[63000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2

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[70000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13

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[76000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1

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[13000]   -fusion SPANNING read extraction for scaff: SLFN11--SLFN12

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[147000]   -fusion SPANNING read extraction for scaff: SOGA3--KIAA0408

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[55000]   
[56000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[32000]   -fusion SPANNING read extraction for scaff: TLK2--AC018638.8

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[17000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 994,
          'seq similar region alignment' => 44554
        };
Execution Time = 0.93 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fusion_preds.coalesced.summary
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -4114.228531
EM: Round [1] log likelihood: -4114.088827
EM: Round [2] log likelihood: -4113.994264
EM: Round [3] log likelihood: -4113.905520
EM: Round [4] log likelihood: -4113.822083
EM: Round [5] log likelihood: -4113.743556
EM: Round [6] log likelihood: -4113.669580
EM: Round [7] log likelihood: -4113.599830
EM: Round [8] log likelihood: -4113.534011
EM: Round [9] log likelihood: -4113.471854
EM: Round [10] log likelihood: -4113.413114
EM: Round [11] log likelihood: -4113.357567
EM: Round [12] log likelihood: -4113.305005
EM: Round [13] log likelihood: -4113.255241
EM: Round [14] log likelihood: -4113.208100
EM: Round [15] log likelihood: -4113.163420
EM: Round [16] log likelihood: -4113.121053
EM: Round [17] log likelihood: -4113.080862
EM: Round [18] log likelihood: -4113.042718
EM: Round [19] log likelihood: -4113.006503
EM: Round [20] log likelihood: -4112.972105
EM: Round [21] log likelihood: -4112.939424
EM: Round [22] log likelihood: -4112.908362
EM: Round [23] log likelihood: -4112.878830
EM: Round [24] log likelihood: -4112.850744
EM: Round [25] log likelihood: -4112.824026
EM: Round [26] log likelihood: -4112.798603
EM: Round [27] log likelihood: -4112.774406
EM: Round [28] log likelihood: -4112.751369
EM: Round [29] log likelihood: -4112.729433
EM: Round [30] log likelihood: -4112.708541
EM: Round [31] log likelihood: -4112.688638
EM: Round [32] log likelihood: -4112.669675
EM: Round [33] log likelihood: -4112.651603
EM: Round [34] log likelihood: -4112.634377
EM: Round [35] log likelihood: -4112.617956
EM: Round [36] log likelihood: -4112.602299
EM: Round [37] log likelihood: -4112.587369
EM: Round [38] log likelihood: -4112.573129
EM: Round [39] log likelihood: -4112.559546
EM: Round [40] log likelihood: -4112.546589
EM: Round [41] log likelihood: -4112.534226
EM: Round [42] log likelihood: -4112.522429
EM: Round [43] log likelihood: -4112.511171
EM: Round [44] log likelihood: -4112.500426
EM: Round [45] log likelihood: -4112.490170
EM: Round [46] log likelihood: -4112.480379
EM: Round [47] log likelihood: -4112.471032
EM: Round [48] log likelihood: -4112.462108
EM: Round [49] log likelihood: -4112.453587
EM: Round [50] log likelihood: -4112.445449
EM: Round [51] log likelihood: -4112.437678
EM: Round [52] log likelihood: -4112.430256
EM: Round [53] log likelihood: -4112.423167
EM: Round [54] log likelihood: -4112.416396
EM: Round [55] log likelihood: -4112.409927
EM: Round [56] log likelihood: -4112.403748
EM: Round [57] log likelihood: -4112.397844
EM: Round [58] log likelihood: -4112.392204
EM: Round [59] log likelihood: -4112.386815
EM: Round [60] log likelihood: -4112.381665
EM: Round [61] log likelihood: -4112.376745
EM: Round [62] log likelihood: -4112.372043
EM: Round [63] log likelihood: -4112.367549
EM: Round [64] log likelihood: -4112.363255
EM: Round [65] log likelihood: -4112.359150
EM: Round [66] log likelihood: -4112.355228
EM: Round [67] log likelihood: -4112.351479
EM: Round [68] log likelihood: -4112.347895
EM: Round [69] log likelihood: -4112.344470
EM: Round [70] log likelihood: -4112.341195
EM: Round [71] log likelihood: -4112.338065
EM: Round [72] log likelihood: -4112.335073
EM: Round [73] log likelihood: -4112.332213
EM: Round [74] log likelihood: -4112.329479
EM: Round [75] log likelihood: -4112.326865
EM: Round [76] log likelihood: -4112.324366
EM: Round [77] log likelihood: -4112.321976
EM: Round [78] log likelihood: -4112.319692
EM: Round [79] log likelihood: -4112.317508
EM: Round [80] log likelihood: -4112.315420
EM: Round [81] log likelihood: -4112.313423
EM: Round [82] log likelihood: -4112.311514
EM: Round [83] log likelihood: -4112.309689
EM: Round [84] log likelihood: -4112.307944
EM: Round [85] log likelihood: -4112.306275
EM: Round [86] log likelihood: -4112.304679
EM: Round [87] log likelihood: -4112.303153
EM: Round [88] log likelihood: -4112.301694
EM: Round [89] log likelihood: -4112.300298
EM: Round [90] log likelihood: -4112.298964
EM: Round [91] log likelihood: -4112.297688
EM: Round [92] log likelihood: -4112.296468
EM: Round [93] log likelihood: -4112.295301
EM: Round [94] log likelihood: -4112.294185
EM: Round [95] log likelihood: -4112.293118
EM: Round [96] log likelihood: -4112.292098
EM: Round [97] log likelihood: -4112.291122
EM: Round [98] log likelihood: -4112.290188
EM: Round [99] log likelihood: -4112.289296
EM: Round [100] log likelihood: -4112.288442
EM: Round [101] log likelihood: -4112.287626
EM: Round [102] log likelihood: -4112.286845
EM: Round [103] log likelihood: -4112.286098
EM: Round [104] log likelihood: -4112.285384
EM: Round [105] log likelihood: -4112.284701
EM: Round [106] log likelihood: -4112.284048
EM: Round [107] log likelihood: -4112.283423
EM: Round [108] log likelihood: -4112.282826
EM: Round [109] log likelihood: -4112.282254
EM: Round [110] log likelihood: -4112.281708
EM: Round [111] log likelihood: -4112.281185
EM: Round [112] log likelihood: -4112.280685
EM: Round [113] log likelihood: -4112.280207
EM: Round [114] log likelihood: -4112.279750
EM: Round [115] log likelihood: -4112.279312
EM: Round [116] log likelihood: -4112.278894
EM: Round [117] log likelihood: -4112.278494
EM: Round [118] log likelihood: -4112.278111
EM: Round [119] log likelihood: -4112.277745
EM: Round [120] log likelihood: -4112.277395
EM: Round [121] log likelihood: -4112.277060
EM: Round [122] log likelihood: -4112.276740
EM: Round [123] log likelihood: -4112.276433
EM: Round [124] log likelihood: -4112.276140
EM: Round [125] log likelihood: -4112.275860
EM: Round [126] log likelihood: -4112.275592
EM: Round [127] log likelihood: -4112.275336
EM: Round [128] log likelihood: -4112.275091
EM: Round [129] log likelihood: -4112.274856
EM: Round [130] log likelihood: -4112.274632
EM: Round [131] log likelihood: -4112.274417
EM: Round [132] log likelihood: -4112.274212
EM: Round [133] log likelihood: -4112.274016
EM: Round [134] log likelihood: -4112.273828
EM: Round [135] log likelihood: -4112.273648
EM: Round [136] log likelihood: -4112.273476
EM: Round [137] log likelihood: -4112.273312
EM: Round [138] log likelihood: -4112.273155
EM: Round [139] log likelihood: -4112.273005
EM: Round [140] log likelihood: -4112.272861
EM: Round [141] log likelihood: -4112.272723
EM: Round [142] log likelihood: -4112.272592
EM: Round [143] log likelihood: -4112.272466
EM: Round [144] log likelihood: -4112.272346
EM: Round [145] log likelihood: -4112.272231
EM: Round [146] log likelihood: -4112.272120
EM: Round [147] log likelihood: -4112.272015
EM: Round [148] log likelihood: -4112.271914
EM: Round [149] log likelihood: -4112.271818
EM: Stopping iterations at round 149 due to insufficient improvement in likelihood.
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/init_EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/prep_igv_extract_junc_reads.ok
Running: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.junction_reads.bam"
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.00 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.junction_reads.bam
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.junction_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/tih_rna_sample_00451_B23WHTKLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/tih_rna_sample_00451_B23WHTKLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/tih_rna_sample_00451_B23WHTKLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/tih_rna_sample_00451_B23WHTKLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.spanning_reads.bam || : 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.spanning_reads.bam || : 
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/tih_rna_sample_00451_B23WHTKLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/tih_rna_sample_00451_B23WHTKLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/tih_rna_sample_00451_B23WHTKLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/tih_rna_sample_00451_B23WHTKLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.consolidated.bam
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.consolidated.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.consolidated.bam
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.consolidated.bam into /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.consolidated.bam.read_coords > /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.21 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/prep_igv_sam_frag_coordss.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.igv.FusionJuncSpan
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.igv.Pfam.gff3 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.igv.Pfam.gff3 
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/prep_igv_pfam_bed.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.igv.seqsimilar.gff3 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/prep_igv_seqsim_bed.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.fa > /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.fa > /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter  --genome_lib_dir ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 50 
CMD: cp /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.post_blast_and_promiscuity_filter
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.Bsc2MN2IDn/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.Bsc2MN2IDn/ctat_genome_lib_build_dir
-done, see /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.Bsc2MN2IDn/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -1981.571271
EM: Round [1] log likelihood: -1981.571271
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1_1.fastp.fastq.gz: 286689991
Execution Time = 5.64 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.fa --gtf /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.gtf  > /tmp/nxf.Bsc2MN2IDn/fi_workdir/microH.dat
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.fa --gtf /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.gtf  > /tmp/nxf.Bsc2MN2IDn/fi_workdir/microH.dat
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.Bsc2MN2IDn/fi_workdir/microH.dat /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.Bsc2MN2IDn/fi_workdir/microH.dat /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.Bsc2MN2IDn --json_outfile /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00451_B23WHTKLT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.Bsc2MN2IDn --json_outfile /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00451_B23WHTKLT4_1
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/create_fi_igvjs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00451_B23WHTKLT4_1 --html_output /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00451_B23WHTKLT4_1 --html_output /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.Bsc2MN2IDn/ctat_genome_lib_build_dir > /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.Bsc2MN2IDn/ctat_genome_lib_build_dir > /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.Bsc2MN2IDn/ctat_genome_lib_build_dir > /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
WARNING, no entry stored in dbm for [ENSG00000281896.1]
WARNING, no entry stored in dbm for [ENSG00000281896.1]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.Bsc2MN2IDn/ctat_genome_lib_build_dir > /tmp/nxf.Bsc2MN2IDn/tih_rna_sample_00451_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.Bsc2MN2IDn/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory